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Georgetown-IR-Lab / QuickUMLS

System for Medical Concept Extraction and Linking
MIT License
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Error while installing #62

Open vishaldeyiiest opened 3 years ago

vishaldeyiiest commented 3 years ago

The readme says that the installation specifically requires UMLS MRCONSO.RRF and MRSTY.RRF. I put these files separately in a new directory and provide it as an argument <umls_installation_path>. When I do python -m quickumls.install <umls_installation_path> <destination_path>, I get the following error: Traceback (most recent call last): File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/runpy.py", line 183, in _run_module_as_main mod_name, mod_spec, code = _get_module_details(mod_name, _Error) File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/runpy.py", line 109, in _get_module_details __import__(pkg_name) File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/site-packages/quickumls/__init__.py", line 1, in <module> from .core import QuickUMLS File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/site-packages/quickumls/core.py", line 17, in <module> from . import toolbox File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/site-packages/quickumls/toolbox.py", line 23, in <module> from quickumls_simstring import simstring File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/site-packages/quickumls_simstring/simstring.py", line 28, in <module> _simstring = swig_import_helper() File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/site-packages/quickumls_simstring/simstring.py", line 24, in swig_import_helper _mod = imp.load_module('_simstring', fp, pathname, description) File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/imp.py", line 243, in load_module return load_dynamic(name, filename, file) File "/users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/imp.py", line 343, in load_dynamic return _load(spec) ImportError: /users/PAS1440/deyosu78/.conda/envs/chemprop/lib/python3.6/site-packages/quickumls_simstring/_simstring.so: undefined symbol: libiconv I don't know how to resolve this? Anyone faced this issue before? Any solution?

soldni commented 3 years ago

Hi @vishaldeyiiest!

Could you provide me with more information about the platform and system you are trying to run QuickUMLS on? it seems like something went wrong during the installation of QuickUMLS, but I am afraid I'd need more info to figure out what exactly.

-Luca

alicerogier555 commented 2 years ago

Hello, I have the same issue. I am on a jupyter server

jupyter --version

" Selected Jupyter core packages... IPython : 7.31.1 ipykernel : 6.13.1 ipywidgets : 7.7.0 jupyter_client : 7.3.3 jupyter_core : 4.10.0 jupyter_server : 1.17.1 jupyterlab : 3.4.3 nbclient : 0.6.4 nbconvert : 6.5.0 nbformat : 5.4.0 notebook : 6.4.12 qtconsole : not installed traitlets : 5.2.2 "

pip --version

" pip 22.2.2 from /opt/conda/envs/rapids/lib/python3.9/site-packages/pip (python 3.9) "

Any solution ?

Thanks in advance

alicerogier555 commented 2 years ago

I resolve the problem by setting the $LD_PRELOAD variable.

jdposada commented 2 years ago

hi @alicerogier555,

Which path did you set on that variable? I have the same issue

alicerogier555 commented 2 years ago

Hello @jdposada,

I set the variable with "/usr/local/lib/libiconv.so" Maybe you should use this command : whereris libiconv to see where libiconv is installed.

Hope this will work for you

jdposada commented 2 years ago

Wow!! that did the trick! this should be highlighted since StackOverflow did not give me a solution for this. Thanks a lot

alicerogier555 commented 2 years ago

Great ! If you are working on a jupyter notebook, don't forget to set the variable also on jupyter (https://github.com/jupyter/notebook/issues/3704 )